I had a problem with running a query and emailed for help and advice. This is the reply I received, others may find this useful:

Thank you for sending this info and your log file to us. From the log
we can see that Google temporarily stopped processing your queries,
which is a result of hammering it too much, and not necessarily only
with WebSite Auditor. Probably you were using another SEO tool before
or simultaneously, and probably that was without human emulation.

Also, when your queries get blocked, this lasts for about two hours,
so if you applied human emulation quickly after you started getting no
results, you probably weren't "unblocked" yet.

I suggest that you turn on human emulation and also use the setting
"Use random user agents" from Preferences -> Search Safety Settings
and run your search again. This should help you.

Please let me know how this works. It is preferable that you contact
us through our support board.